Has anyone used Circa to plot MBD-seq data?
I'm struggling getting my data into the required format for Circa. Honestly don't even know which file type to start with to get the seq data into column/row format for Circa. Can anyone help me here?
Current file formats I have include: SAM, BAM, and BigWig.
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That's commercial software right? Then you should ask the company for help... given that it would cost me $100 to buy it, small chance you'll find a lot of users here.
Do you mean Circa tool? If yes, then you should maybe have a look at the tutorials on their website or contact the developers directly as it is a commercial tool that not many people would have tried/bought.
Yes, it is the Circa software. It's not the software that I need help with though. What I need to do is get my files into an Excel friendly format so I can get the data into Circa.
Yikes!
Consider using Circos instead, if Circa requires you to do that.
On a serious note BED format should work. Circa seems to have a tutorial for the inputs.
I've tried Circos and it's a disaster. Bioinformatics isn't my specialty and I don't want to spend weeks trying to figure that out.
bam2bedfrom BEDOPS can be one option here. You will need to use it on the command line though.